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BioC 3.2: BUILD BIN report for VegaMC on oaxaca

This page was generated on 2016-03-15 11:14:01 -0700 (Tue, 15 Mar 2016).

Package 1087/1104HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
VegaMC 3.8.1
Sandro Morganella
Snapshot Date: 2016-03-14 16:20:11 -0700 (Mon, 14 Mar 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/VegaMC
Last Changed Rev: 114203 / Revision: 114766
Last Changed Date: 2016-03-03 01:46:05 -0800 (Thu, 03 Mar 2016)
zin1 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK  ERROR 
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  NotNeeded  OK  ERROR  OK 
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  ERROR [ OK ]

Summary

Package: VegaMC
Version: 3.8.1
Command: rm -rf VegaMC.buildbin-libdir && mkdir VegaMC.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh VegaMC_3.8.1.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R VegaMC.buildbin-libdir
StartedAt: 2016-03-15 05:52:31 -0700 (Tue, 15 Mar 2016)
EndedAt: 2016-03-15 05:52:46 -0700 (Tue, 15 Mar 2016)
EllapsedTime: 14.8 seconds
RetCode: 0
Status:  OK 
PackageFile: VegaMC_3.8.1.tgz
PackageFileSize: 1.78 MiB

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf VegaMC.buildbin-libdir && mkdir VegaMC.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh VegaMC_3.8.1.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R VegaMC.buildbin-libdir
###
##############################################################################
##############################################################################


>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=VegaMC.buildbin-libdir VegaMC_3.8.1.tar.gz'
>>>>>>> 

* installing *source* package ‘VegaMC’ ...
** libs
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c run_vegaMC.c -o run_vegaMC.o
run_vegaMC.c:491:27: warning: expression which evaluates to zero treated as a null pointer constant of type 'char *' [-Wnon-literal-null-conversion]
            elem = strtok('\0', sep);
                          ^˜˜˜
run_vegaMC.c:526:27: warning: expression which evaluates to zero treated as a null pointer constant of type 'char *' [-Wnon-literal-null-conversion]
            elem = strtok('\0', sep);
                          ^˜˜˜
run_vegaMC.c:618:18: warning: unused variable 'brkt' [-Wunused-variable]
    char *elem, *brkt;
                 ^
3 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c sort_data.c -o sort_data.o
sort_data.c:131:27: warning: expression which evaluates to zero treated as a null pointer constant of type 'char *' [-Wnon-literal-null-conversion]
            elem = strtok('\0', sep);
                          ^˜˜˜
sort_data.c:180:27: warning: expression which evaluates to zero treated as a null pointer constant of type 'char *' [-Wnon-literal-null-conversion]
            elem = strtok('\0', sep);
                          ^˜˜˜
2 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c vegaMC.c -o vegaMC.o
clang -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o VegaMC.so run_vegaMC.o sort_data.o vegaMC.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.2-bioc/meat/VegaMC.buildbin-libdir/VegaMC/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (VegaMC)


>>>>>>> 
>>>>>>> FIXING LINKS FOR VegaMC.buildbin-libdir/VegaMC/libs//VegaMC.so
>>>>>>> 

install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/3.2/Resources/lib/libgcc_s.1.dylib" "VegaMC.buildbin-libdir/VegaMC/libs//VegaMC.so"
install_name_tool -change "/usr/local/lib/libgfortran.3.dylib" "/Library/Frameworks/R.framework/Versions/3.2/Resources/lib/libgfortran.3.dylib" "VegaMC.buildbin-libdir/VegaMC/libs//VegaMC.so"
install_name_tool -change "/usr/local/lib/libreadline.5.2.dylib" "/Library/Frameworks/R.framework/Versions/3.2/Resources/lib/libreadline.5.2.dylib" "VegaMC.buildbin-libdir/VegaMC/libs//VegaMC.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/3.2/Resources/lib/libreadline.dylib" "VegaMC.buildbin-libdir/VegaMC/libs//VegaMC.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/3.2/Resources/lib/libquadmath.0.dylib" "VegaMC.buildbin-libdir/VegaMC/libs//VegaMC.so"